The Sequence page within the Coverage page of the Protein Identification Details view includes a protein sequence coverage bar and a sequence table. The page displays a graphical and a textual representation of the protein sequence, its coverage with identified peptides, and a list of all found PTMs. The peptide identifications are color-coded to reflect their respective identification confidence.
| No. | Description | No. | Description |
|---|---|---|---|
1 | Protein sequence coverage bar | 3 | UniProt database annotation |
2 | Sequence table | 4 | PTM annotation |
For more information about the parameters of the Sequences page, see Parameters on the Coverage page of the Protein Identification Details view.
| No. | Description | No. | Description |
|---|---|---|---|
1 | List of modifications found for the protein | 3 | Corresponding underlined sequence |
2 | Selected colored bar |
The application annotates the protein sequence with each PTM found in the search by placing the modification’s single-letter abbreviation above the sequence. It displays all modifications of PSMs passing the active filters. In some cases, the modification displayed above a PSM of high confidence might only be found in a redundantly identified PSM of medium or low confidence.
The Protein Annotation node retrieves UniProt database information, including PTMs, from Protein and saves it in the application results files (see Adding Protein Annotation to a Workflow).
If this annotation information is available and you select the Annotate PTMs Reported in the UniProt checkbox in the Protein Identification Details view, the modification appears as a single-letter abbreviation in a gray box beneath the amino acids of the protein in the sequence table.
When you use the ptmRS node in the processing workflow, PTM site localization scores are available for all PTMs, including phosphorylation. In this case, the application displays the found phosphorylation modifications above portions of the amino acid sequences and color-codes their boxes to indicate the probability of the modification being found on those portions. A legend explaining the color-coding appears in the PTM Site Probabilities area to the left of the sequence table.
The following figure shows a phosphorylation color-coded in green boxes and red boxes to indicate differing probabilities of occurrence at that site.
| No. | Description | No. | Description |
|---|---|---|---|
1 | Likelihood of phosphorylation occurring at this site is 45 to 75 percent. | 3 | Likelihood of phosphorylation occurring at this site is 25 to 45 percent. |
2 | Likelihood of phosphorylation occurring at this site is 99 to 100 percent. | 4 | Likelihood of phosphorylation occurring at this site is 75 to 99 percent. |
The Proteome Discoverer annotations and the UniProt database annotations together in the sequence table might indicate the following:
Example annotation | Description |
|---|---|
| The modification is annotated and found in the MS experiment. |
| The modification is annotated but not found in the MS experiment. |
| The modification is annotated, but the peptide was not identified in the MS experiment. There are no results, so no information is available about the modification. |
| The modification is found but not annotated in the UniProt database. Either the modification is known but not annotated in the database, or the modification at this position is currently unknown and might be worth further investigation. |
Amino acids in the protein sequence are assigned sequential numbers. The numbers in the dark blue column to the left of the sequence table and the numbers in the dark blue header on top of the sequence table are intended to orient you when you want to find automatically assigned amino acid numbers in the table. The application displays numbers in the left column in increments of 100, and they correspond to the numbers on top of the protein sequence coverage bar. The application displays numbers on top of the table in increments of 10. In the 11–20 column, the first row displays the 11th to 20th amino acid, the second row displays the 111th to 120th amino acid, and so on. For example, the protein sequence contains 1,007 amino acids, so the numbers to the left of the table extend from 1 to 991, and the numbers across the top of the table extend from 1 to 17.